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PURPOSE: Small cell lung cancer (SCLC) is characterized by rapid progression after platinum resistance. Circulating tumor (ctDNA) dynamics early in treatment may help determine platinum sensitivity. MATERIALS AND METHODS: Serial plasma samples were collected from patients receiving platinum-based chemotherapy for SCLC on the first 3 days of cycle one and on the first days of subsequent cycles with paired samples collected both before and again after infusions. Tumor-informed plasma analysis was carried out using CAncer Personalized Profiling by deep Sequencing (CAPP-Seq). The mean variant allele frequency (VAF) of all pretreatment mutations was tracked in subsequent blood draws and correlated with radiologic response. RESULTS: ctDNA kinetics were assessed in 122 samples from 21 patients. Pretreatment VAF did not differ significantly between patients who did and did not respond to chemotherapy (mean 22.5% v 4.6%, P =.17). A slight increase in ctDNA on cycle 1, day 1 immediately post-treatment was seen in six of the seven patients with available draws (fold change from baseline: 1.01-1.44), half of whom achieved a response. All patients who responded had a >2-fold decrease in mean VAF on cycle 2 day 1 (C2D1). Progression-free survival (PFS) and overall survival (OS) were significantly longer in patients with a >2-fold decrease in mean VAF after one treatment cycle (6.8 v 2.6 months, log-rank P =.0004 and 21.7 v 6.4 months, log rank P =.04, respectively). CONCLUSION: A >2-fold decrease in ctDNA concentration was observed by C2D1 in all patients who were sensitive to platinum-based therapy and was associated with longer PFS and OS. [ABSTRACT FROM AUTHOR]

PURPOSE: Small cell lung cancer (SCLC) is characterized by rapid progression after platinum resistance. Circulating tumor (ctDNA) dynamics early in treatment may help determine platinum sensitivity. MATERIALS AND METHODS: Serial plasma samples were collected from patients receiving platinum-based chemotherapy for SCLC on the first 3 days of cycle one and on the first days of subsequent cycles with paired samples collected both before and again after infusions. Tumor-informed plasma analysis was carried out using CAncer Personalized Profiling by deep Sequencing (CAPP-Seq). The mean variant allele frequency (VAF) of all pretreatment mutations was tracked in subsequent blood draws and correlated with radiologic response. RESULTS: ctDNA kinetics were assessed in 122 samples from 21 patients. Pretreatment VAF did not differ significantly between patients who did and did not respond to chemotherapy (mean 22.5% v 4.6%, P =.17). A slight increase in ctDNA on cycle 1, day 1 immediately post-treatment was seen in six of the seven patients with available draws (fold change from baseline: 1.01-1.44), half of whom achieved a response. All patients who responded had a >2-fold decrease in mean VAF on cycle 2 day 1 (C2D1). Progression-free survival (PFS) and overall survival (OS) were significantly longer in patients with a >2-fold decrease in mean VAF after one treatment cycle (6.8 v 2.6 months, log-rank P =.0004 and 21.7 v 6.4 months, log rank P =.04, respectively). CONCLUSION: A >2-fold decrease in ctDNA concentration was observed by C2D1 in all patients who were sensitive to platinum-based therapy and was associated with longer PFS and OS. [ABSTRACT FROM AUTHOR]

Consensus guidelines recommend use of granulocyte colony stimulating factor in patients deemed at risk of chemotherapy‐induced neutropenia, however, these risk models are limited in the factors they consider and miss some cases of neutropenia. Clinical decision making could be supported using models that better tailor their predictions to the individual patient using the wealth of data available in electronic health records (EHRs). Here, we present a hybrid pharmacokinetic/pharmacodynamic (PKPD)/machine learning (ML) approach that uses predictions and individual Bayesian parameter estimates from a PKPD model to enrich an ML model built on her data. We demonstrate this approach using models developed on a large real‐world data set of 9121 patients treated for lymphoma, breast, or thoracic cancer. We also investigate the benefits of augmenting the training data using synthetic data simulated with the PKPD model. We find that PKPD‐enrichment of ML models improves prediction of grade 3–4 neutropenia, as measured by higher precision (61%) and recall (39%) compared to PKPD model predictions (47%, 33%) or base ML model predictions (51%, 31%). PKPD augmentation of ML models showed minor improvements in recall (44%) but not precision (56%), and data augmentation required careful tuning to control overfitting its predictions to the PKPD model. PKPD enrichment of ML shows promise for leveraging both the physiology‐informed predictions of PKPD and the ability of ML to learn predictor‐outcome relationships from large data sets to predict patient response to drugs in a clinical precision dosing context. [ABSTRACT FROM AUTHOR]

Up to 50% of patients with non-small cell lung cancer (NSCLC) develop brain metastasis (BM), yet the study of BM genomics has been limited by tissue access, incomplete clinical data, and a lack of comparison with paired extracranial specimens. Here we report a cohort of 233 patients with resected and sequenced (MSK-IMPACT) NSCLC BM and comprehensive clinical data. With matched samples (47 primary tumor, 42 extracranial metastatic), we show CDKN2A/B deletions and cell cycle pathway alterations to be enriched in the BM samples. Meaningful clinico-genomic correlations are noted, namely EGFR alterations in leptomeningeal disease (LMD) and MYC amplifications in multifocal regional brain progression. Patients who developed early LMD frequently have had uncommon, multiple, and persistently detectable EGFR driver mutations. The distinct mutational patterns identified in BM specimens compared to other tissue sites suggest specific biologic underpinnings of intracranial progression. The genomic landscape of brain metastasis (BM) in patients with non-small cell lung cancer (NSCLC) remains to be explored. Here, the authors analyse a cohort of 233 patients with BM including 47 primary tumour, 42 extracranial metastatic matched samples and reveal distinct mutational patterns. [ABSTRACT FROM AUTHOR]

A myriad of organ-specific complications have been observed with COVID-19. While racial/ethnic minorities have been disproportionately burdened by this disease, our understanding of the unique risk factors for complications among a diverse population of cancer patients remains limited. This is a multi-institutional, multi-ethnic cohort study evaluating COVID-19 complications among cancer patients. Patients with an invasive cancer diagnosis and confirmed SARS-CoV-2 infection were identified from March to November 2020. Demographic and clinical data were obtained and a multivariate logistic regression was employed to evaluate the impact of demographic and clinical factors on COVID-19 complications. The study endpoints were evaluated independently and included any complication, sepsis, pulmonary complications and cardiac complications. A total of 303 patients were evaluated, of whom 48% were male, 79% had solid tumors, and 42% were Hispanic/Latinx (Hispanic). Malignant hematologic cancers were associated with a higher risk of sepsis (OR 3.93 (95% CI 1.58–9.81)). Male patients had a higher risk of sepsis (OR 4.42 (95% CI 1.63–11.96)) and cardiac complications (OR 2.02 (95% CI 1.05–3.89)). Hispanic patients had a higher odds of any complication (OR 2.31 (95% CI 1.18–4.51)) and other race was associated with a higher odds of cardiac complications (OR 2.41 (95% CI 1.01–5.73)). Clinically, fever, cough, and ≥2 co-morbidities were independently significantly associated with any complication. This analysis evaluated covariates that can significantly predict a myriad of complications among a multi-ethnic cohort of cancer patients. The conclusions drawn from this analysis elucidate a mechanistic understanding of differential illness severity from COVID-19. [ABSTRACT FROM AUTHOR]

Purpose: Chemotherapy with or without immunotherapy remains the mainstay of treatment for triple-negative breast cancer (TNBC). A subset of TNBCs express the androgen receptor (AR), representing a potential new therapeutic target. This study assessed the feasibility of adjuvant enzalutamide, an AR antagonist, in early-stage, AR-positive (AR +) TNBC. Methods: This study was a single-arm, open-label, multicenter trial in which patients with stage I–III, AR ≥ 1% TNBC who had completed standard-of-care therapy were treated with enzalutamide 160 mg/day orally for 1 year. The primary objective of this study was to evaluate the feasibility of 1 year of adjuvant enzalutamide, defined as the treatment discontinuation rate of enzalutamide due to toxicity, withdrawal of consent, or other events related to tolerability. Secondary endpoints included disease-free survival (DFS), overall survival (OS), safety, and genomic features of recurrent tumors. Results: Fifty patients were enrolled in this study. Thirty-five patients completed 1 year of therapy, thereby meeting the prespecified trial endpoint for feasibility. Thirty-two patients elected to continue with an optional second year of treatment. Grade ≥ 3 treatment-related adverse events were uncommon. The 1-year, 2-year, and 3-year DFS were 94%, 92% , and 80%, respectively. Median OS has not been reached. Conclusion: This clinical trial demonstrates that adjuvant enzalutamide is a feasible and well-tolerated regimen in patients with an early-stage AR + TNBC. Randomized trials in the metastatic setting may inform patient selection through biomarker development; longer follow-up is needed to determine the effect of anti-androgens on DFS and OS in this patient population. [ABSTRACT FROM AUTHOR]

Endocrine therapy (ET) is a pivotal strategy to manage early- and advanced-stage estrogen receptor-positive (ER+) breast cancer. In patients with metastatic breast cancer (MBC), progression of disease inevitably occurs due to the presence of acquired or intrinsic resistance mechanisms. ET resistance can be driven by ligand-independent, ER-mediated signaling that promotes tumor proliferation in the absence of hormone, or ER-independent oncogenic signaling that circumvents endocrine regulated transcription pathways. Estrogen receptor 1 (ESR1) mutations induce constitutive ER activity and upregulate ER-dependent gene transcription, provoking resistance to estrogen deprivation and aromatase inhibitor therapy. The role ESR1 mutations play in regulating response to other therapies, such as the selective estrogen receptor degrader (SERD) fulvestrant and the available CDK4/6 inhibitors, is less clear. Novel oral SERDs and other next-generation ETs are in clinical development for ER+ breast cancer as single agents and in combination with established targeted therapies. Recent results from the phase III EMERALD trial demonstrated improved outcomes with the oral SERD elacestrant compared to standard anti-estrogen therapies in ER+ MBC after prior progression on ET, and other agents have shown promise in both the laboratory and early-phase clinical trials. In this review, we will discuss the emerging data related to oral SERDs and other novel ET in managing ER+ breast cancer. As clinical data continue to mature on these next-generation ETs, important questions will emerge related to the optimal sequence of therapeutic options and the genomic and molecular landscape of resistance to these agents. [ABSTRACT FROM AUTHOR]

Inhibition of HER2 in HER2-amplified breast cancer has been remarkably successful clinically, as demonstrated by the efficacy of HER-kinase inhibitors and HER2-antibody treatments. Whilst resistance to HER2 inhibition is common in the metastatic setting, the specific programs downstream of HER2 driving resistance are not established. Through genomic profiling of 733 HER2-amplified breast cancers, we identify enrichment of somatic alterations that promote MEK/ERK signaling in metastatic tumors with shortened progression-free survival on anti-HER2 therapy. These mutations, including NF1 loss and ERBB2 activating mutations, are sufficient to mediate resistance to FDA-approved HER2 kinase inhibitors including tucatinib and neratinib. Moreover, resistant tumors lose AKT dependence while undergoing a dramatic sensitization to MEK/ERK inhibition. Mechanistically, this driver pathway switch is a result of MEK-dependent activation of CDK2 kinase. These results establish genetic activation of MAPK as a recurrent mechanism of anti-HER2 therapy resistance that may be effectively combated with MEK/ERK inhibitors. Resistance to HER2 inhibition in HER2- amplified breast cancer is common in the metastatic setting and the underlying molecular mechanisms remain unknown. Here, the authors, perform genomic profiling of 733 HER2-amplified breast cancers and propose genetic activation of MAPK as a resistance mechanism. [ABSTRACT FROM AUTHOR]

Activating mutations in PIK3CA are frequently found in estrogen-receptor-positive (ER+) breast cancer, and the combination of the phosphatidylinositol 3-kinase (PI3K) inhibitor alpelisib with anti-ER inhibitors is approved for therapy. We have previously demonstrated that the PI3K pathway regulates ER activity through phosphorylation of the chromatin modifier KMT2D. Here, we discovered a methylation site on KMT2D, at K1330 directly adjacent to S1331, catalyzed by the lysine methyltransferase SMYD2. SMYD2 loss attenuates alpelisib-induced KMT2D chromatin binding and alpelisib-mediated changes in gene expression, including ER-dependent transcription. Knockdown or pharmacological inhibition of SMYD2 sensitizes breast cancer cells, patient-derived organoids, and tumors to PI3K/AKT inhibition and endocrine therapy in part through KMT2D K1330 methylation. Together, our findings uncover a regulatory crosstalk between post-translational modifications that fine-tunes KMT2D function at the chromatin. This provides a rationale for the use of SMYD2 inhibitors in combination with PI3Kα/AKT inhibitors in the treatment of ER+/ PIK3CA mutant breast cancer. [Display omitted] • KMT2D is methylated at K1330 by SMYD2 • There is crosstalk between phosphorylation of KMT2D at S1331 and methylation at K1330 • Loss of SMYD2 abrogates PI3Ki-induced KMT2D chromatin binding and ER-dependent transcription • Inhibition of KMT2D methylation sensitizes cells and tumors to PI3K/AKT inhibition Blawski et al. show that KMT2D is methylated by the lysine methyltransferase SMYD2 at K1330. SMYD2 loss attenuates PI3K inhibitor-induced KMT2D chromatin binding at estrogen-receptor (ER) loci and ER-dependent transcription. SMYD2 inhibition sensitizes cells, patient-derived organoids, and tumors to PI3K/AKT inhibition and endocrine therapy through KMT2D K1330 methylation. [ABSTRACT FROM AUTHOR]

PURPOSE: Key oncology end points are not routinely encoded into electronic medical records (EMRs). We assessed whether natural language processing (NLP) can abstract treatment discontinuation rationale from unstructured EMR notes to estimate toxicity incidence and progression-free survival (PFS). METHODS: We constructed a retrospective cohort of 6,115 patients with early-stage and 701 patients with metastatic breast cancer initiating care at Memorial Sloan Kettering Cancer Center from 2008 to 2019. Each cohort was divided into training (70%), validation (15%), and test (15%) subsets. Human abstractors identified the clinical rationale associated with treatment discontinuation events. Concatenated EMR notes were used to train high-dimensional logistic regression and convolutional neural network models. Kaplan-Meier analyses were used to compare toxicity incidence and PFS estimated by our NLP models to estimates generated by manual labeling and time-to-treatment discontinuation (TTD). RESULTS: Our best high-dimensional logistic regression models identified toxicity events in early-stage patients with an area under the curve of the receiver-operator characteristic of 0.857 ± 0.014 (standard deviation) and progression events in metastatic patients with an area under the curve of 0.752 ± 0.027 (standard deviation). NLP-extracted toxicity incidence and PFS curves were not significantly different from manually extracted curves (P =.95 and P =.67, respectively). By contrast, TTD overestimated toxicity in early-stage patients (P <.001) and underestimated PFS in metastatic patients (P <.001). Additionally, we tested an extrapolation approach in which 20% of the metastatic cohort were labeled manually, and NLP algorithms were used to abstract the remaining 80%. This extrapolated outcomes approach resolved PFS differences between receptor subtypes (P <.001 for hormone receptor+/human epidermal growth factor receptor 2− v human epidermal growth factor receptor 2+ v triple-negative) that could not be resolved with TTD. CONCLUSION: NLP models are capable of abstracting treatment discontinuation rationale with minimal manual labeling. [ABSTRACT FROM AUTHOR]

PURPOSE: Cell-free DNA (cfDNA) analysis offers a noninvasive means to access the tumor genome. Despite limited sensitivity of broad-panel sequencing for detecting low-frequency mutations in cfDNA, it may enable more comprehensive genomic characterization in patients with sufficiently high disease burden. We investigated the utility of large-panel cfDNA sequencing in patients enrolled to a Phase I AKT1 -mutant solid tumor basket study. METHODS: Patients had AKT1 E17K-mutant solid tumors and were treated on the multicenter basket study (ClinicalTrials.gov identifier: NCT01226316) of capivasertib, an AKT inhibitor. Serial plasma samples were prospectively collected and sequenced using exon-capture next-generation sequencing (NGS) analysis of 410 genes (Memorial Sloan Kettering [MSK]-Integrated Molecular Profiling of Actionable Cancer Target [IMPACT]) and allele-specific droplet digital polymerase chain reaction (ddPCR) for AKT1 E17K. Tumor DNA (tDNA) NGS (MSK-IMPACT) was also performed on available pretreatment tissue biopsy specimens. RESULTS: Among 25 patients, pretreatment plasma samples were sequenced to an average coverage of 504×. Somatic mutations were called in 20/25 (80%), with mutant allele fractions highly concordant with ddPCR of AKT1 E17K (r 2 = 0.976). Among 17 of 20 cfDNA-positive patients with available tDNA for comparison, mutational concordance was acceptable, with 82% of recurrent mutations shared between tissue and plasma. cfDNA NGS captured additional tumor heterogeneity, identifying mutations not observed in tDNA in 38% of patients, and revealed oncogenic mutations in patients without available baseline tDNA. Longitudinal cfDNA NGS (n = 98 samples) revealed distinct patterns of clonal dynamics in response to therapy. CONCLUSION: Large gene panel cfDNA NGS is feasible for patients with high disease burden and is concordant with single-analyte approaches, providing a robust alternative to ddPCR with greater breadth. cfDNA NGS can identify heterogeneity and potentially biologically informative and clinically relevant alterations. [ABSTRACT FROM AUTHOR]

Aims: The American Society of Clinical Oncology/College of American Pathologists (ASCO/CAP) updated the testing guideline in 2018 to address issues arising from uncommon human epidermal growth factor receptor 2 (HER2) fluorescence in‐situ hybridisation (FISH) results according to the 2013 guideline. Next‐generation sequencing (NGS) may be used to better classify patients. The aim of this study was to assess the ERBB2 amplification status of invasive breast carcinoma with equivocal HER2 immunohistochemistry (IHC) results by using NGS, focusing on Group 4 (HER2/CEP17 ratio of <2.0; average HER2 signals/cell of ≥4.0 and <6.0). Methods and results: We retrospectively reviewed HER2 FISH and NGS data of HER2 IHC‐equivocal breast carcinomas at our centre between January 2009 and September 2019, wherein all three assays were performed on the same tissue block, and compared HER2 FISH results, according to the 2018 ASCO/CAP guideline, and the ERBB2 amplification status determined with NGS. A total of 52 HER2 FISH and NGS results from 51 patients with HER2 IHC‐equivocal breast carcinomas were reviewed. The cohort included eight cases classified as 2018 ASCO/CAP in‐situ hybridisation Group 1, three classified as Group 2, three classified as Group 3, 14 classified as Group 4, and 24 classified as Group 5. Thirteen of 14 (92.9%) Group 4 (HER2‐negative) cases were classified as ERBB2‐non‐amplified by the use of NGS; the discordant case was later classified as Group 1 with alternative sample FISH testing. NGS revealed no significant difference in somatic mutations or copy number alterations between Groups 4 and 5. Conclusions: Our NGS findings support the reclassification of HER2 FISH‐equivocal cases as HER2‐negative under the 2018 ASCO/CAP guideline. [ABSTRACT FROM AUTHOR]

PURPOSE: Cell-free DNA (cfDNA) analysis offers a noninvasive means to access the tumor genome. Despite limited sensitivity of broad-panel sequencing for detecting low-frequency mutations in cfDNA, it may enable more comprehensive genomic characterization in patients with sufficiently high disease burden. We investigated the utility of large-panel cfDNA sequencing in patients enrolled to a Phase I AKT1 -mutant solid tumor basket study. METHODS: Patients had AKT1 E17K-mutant solid tumors and were treated on the multicenter basket study (ClinicalTrials.gov identifier: NCT01226316) of capivasertib, an AKT inhibitor. Serial plasma samples were prospectively collected and sequenced using exon-capture next-generation sequencing (NGS) analysis of 410 genes (Memorial Sloan Kettering [MSK]-Integrated Molecular Profiling of Actionable Cancer Target [IMPACT]) and allele-specific droplet digital polymerase chain reaction (ddPCR) for AKT1 E17K. Tumor DNA (tDNA) NGS (MSK-IMPACT) was also performed on available pretreatment tissue biopsy specimens. RESULTS: Among 25 patients, pretreatment plasma samples were sequenced to an average coverage of 504×. Somatic mutations were called in 20/25 (80%), with mutant allele fractions highly concordant with ddPCR of AKT1 E17K (r 2 = 0.976). Among 17 of 20 cfDNA-positive patients with available tDNA for comparison, mutational concordance was acceptable, with 82% of recurrent mutations shared between tissue and plasma. cfDNA NGS captured additional tumor heterogeneity, identifying mutations not observed in tDNA in 38% of patients, and revealed oncogenic mutations in patients without available baseline tDNA. Longitudinal cfDNA NGS (n = 98 samples) revealed distinct patterns of clonal dynamics in response to therapy. CONCLUSION: Large gene panel cfDNA NGS is feasible for patients with high disease burden and is concordant with single-analyte approaches, providing a robust alternative to ddPCR with greater breadth. cfDNA NGS can identify heterogeneity and potentially biologically informative and clinically relevant alterations. [ABSTRACT FROM AUTHOR]

Purpose: Rash develops in approximately 50% of patients receiving alpelisib for breast cancer, often requiring dose modifications. Here, we describe the clinicopathologic, laboratory, and management characteristics of alpelisib-related dermatologic adverse events (dAEs). Methods: A single center-retrospective analysis was conducted. Data were abstracted from electronic medical records. Results: A total of 102 patients (mean age 56 years, range 27–83) receiving alpelisib most frequently in combination with endocrine therapy (79, 77.5%) were included. We identified 41 (40.2%) patients with all-grade rash distributed primarily along the trunk (78%) and extremities (70%) that developed approximately within two weeks of treatment initiation (mean 12.8 ± 1.5 days) and lasted one-week (mean duration 7.1 ± 0.8 days). Of 29 patients with documented morphology of alpelisib-related dAEs, 26 (89.7%) had maculopapular rash. Histology showed perivascular and interface lymphocytic dermatitis. All-grade rash correlated with an increase in serum eosinophils from 2.7 to 4.4%, p < 0.05, and prophylaxis with non-sedating antihistamines (n = 43) was correlated with a reduction of grade 1/2 rash (OR 0.39, p = 0.09). Sixteen (84.2%) of 19 patients with grade 3 dAEs resulted in interruption of alpelisib, which were managed with antihistamines, topical and systemic corticosteroids. We did not observe rash recurrence in 12 (75%) patients who were re-challenged. Conclusions: A maculopapular rash associated with increased blood eosinophils occurs frequently with alpelisib. While grade 3 rash leads to alpelisib therapy interruption, dermatologic improvement is evident with systemic corticosteroids; and most patients can continue oncologic treatment at a maintained or reduced dose upon re-challenge with alpelisib. [ABSTRACT FROM AUTHOR]

This study presents experimental and simulation results for edge‐coupled waveguide unitravelling‐carrier (UTC) photodiodes based on an InGaAs/InP heterostructure. Experimental results are used to calibrate the numerical device simulator. The authors study how different aspects of the UTC photodiode epistructure and contacts impact on the overall device bandwidth, calculating the photoresponse for different structural parameters and doping concentration profiles. The effect of these parameters on the 3‐dB cut‐off frequency is studied, and design guidelines for UTC photodiodes with improved performance are presented. The UTC photodiode simulated using authors' design guidelines has a 3 dB cut‐off frequency of 49 GHz, a factor of 2 larger than the 25 GHz cut‐off of the fabricated UTC photodiode. [ABSTRACT FROM AUTHOR]

The performance of germanium and silicon inversion-mode and junctionless nanowire field-effect transistors are investigated using three-dimensional quantum mechanical simulations in the ballistic transport regime and within the framework of effective-mass theory for different channel materials and orientations. Our study shows that junctionless nanowire transistors made using n-type Ge or Si nanowires as a channel material are more immune to short-channel effects than conventional inversion-mode nanowire field-effect transistors. As a result, these transistors present smaller subthreshold swing, less drain-induced barrier-lowering, lower source-to-drain tunneling, and higher Ion/Ioff ratio for the same technology node and low standby power technologies. We also show that the short-channel characteristics of Ge and Si junctionless nanowire transistors, unlike the inversion-mode nanowire transistors, are very similar. The results are explained through a detailed analysis on the effect of the channel crystallographic orientation, effective masses, and dielectric constant on electrical characteristics. [ABSTRACT FROM AUTHOR]

In this paper we investigate the effects of intravalley acoustic phonon scattering on the quantum transport and on the electrical characteristics of multigate silicon nanowire metal-oxide-semiconductor field-effect transistors. We show that acoustic phonons cause a shift and broadening of the local DOS in the nanowire, which modifies the electrical characteristics of the device. The influence of scattering on off-state and on-state currents is investigated for different values of channel length. In the ballistic transport regime, source-to-drain tunneling current is predominant, whereas in the presence of acoustic phonons, diffusion becomes the dominant current transport mechanism. A three-dimensional quantum mechanical device simulator based on the nonequilibrium Green’s function formalism in uncoupled-mode space has been developed to extract device parameters in the presence of electron–phonon interactions. Electron–phonon scattering is accounted for by adopting the self-consistent Born approximation and using the deformation potential theory. [ABSTRACT FROM AUTHOR]

This study presents experimental and simulation results for edge-coupled waveguide unitravelling-carrier (UTC) photodiodes based on an InGaAs/InP heterostructure. Experimental results are used to calibrate the numerical device simulator. The authors study how different aspects of the UTC photodiode epistructure and contacts impact on the overall device bandwidth, calculating the photoresponse for different structural parameters and doping concentration profiles. The effect of these parameters on the 3-dB cut-off frequency is studied, and design guidelines for UTC photodiodes with improved performance are presented. The UTC photodiode simulated using authors' design guidelines has a 3 dB cut-off frequency of 49 GHz, a factor of 2 larger than the 25 GHz cut-off of the fabricated UTC photodiode. [ABSTRACT FROM AUTHOR]

PURPOSE: Biliary tract cancers (BTCs), which include intrahepatic cholangiocarcinoma (ICC), extrahepatic cholangiocarcinoma (EHC), and gallbladder cancer (GBC), have limited treatment options. We sought to comprehensively examine the clinical and molecular characteristics of BTCs with amplification or mutation of ERBB2. METHODS: Demographic, outcome, and treatment response data were collected for patients with ERBB2 -altered BTC identified by next-generation sequencing with Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets from 2014 to 2018. RESULTS: A total of 517 patients with BTC underwent next-generation sequencing (ICC, n = 313; EHC, n = 93; GBC, n = 111). Twenty-eight patients (5.4%) had ERBB2 alterations, including 2.7% with ERBB2 gene amplification, 2.3% with ERBB2 mutation, and 0.4% with concurrent amplification and mutation. The prevalence of ERBB2 gene alterations was significantly higher in GBC (12.6%) than in ICC (2.2%) and EHC (7.5%; P <.001). In ERBB2- amplified tumors, the median fold change was 6.4 (range, 2.1 to 19.7), while in ERBB2 -mutant tumors, the most frequent mutated domain was the extracellular domain (32%), with all mutations in this region involving the S310 codon. Frequent co-altered genes in this cohort were TP53 (54%), PIK3CA (21%), and CDKN2A (18%); KRAS amplification/mutation was found in 7% of patients. One patient with ERBB2 -amplified EHC who enrolled in a basket trial (ClinicalTrials.gov identifier: NCT02675829) had a partial response to the human epidermal growth factor receptor 2–targeted antibody-drug conjugate ado-trastuzumab emtansine. CONCLUSION: ERBB2 alterations are present in 5.4% of BTCs. When present, the degree of ERBB2 gene amplification is often high, and S310 codon mutations are the most common hotspot. These features, along with the presented case, support further development of human epidermal growth factor receptor 2–targeted therapy in ERBB2 -mutant and/or -amplified BTC. [ABSTRACT FROM AUTHOR]

PURPOSE: Biliary tract cancers (BTCs), which include intrahepatic cholangiocarcinoma (ICC), extrahepatic cholangiocarcinoma (EHC), and gallbladder cancer (GBC), have limited treatment options. We sought to comprehensively examine the clinical and molecular characteristics of BTCs with amplification or mutation of ERBB2. METHODS: Demographic, outcome, and treatment response data were collected for patients with ERBB2 -altered BTC identified by next-generation sequencing with Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets from 2014 to 2018. RESULTS: A total of 517 patients with BTC underwent next-generation sequencing (ICC, n = 313; EHC, n = 93; GBC, n = 111). Twenty-eight patients (5.4%) had ERBB2 alterations, including 2.7% with ERBB2 gene amplification, 2.3% with ERBB2 mutation, and 0.4% with concurrent amplification and mutation. The prevalence of ERBB2 gene alterations was significantly higher in GBC (12.6%) than in ICC (2.2%) and EHC (7.5%; P <.001). In ERBB2- amplified tumors, the median fold change was 6.4 (range, 2.1 to 19.7), while in ERBB2 -mutant tumors, the most frequent mutated domain was the extracellular domain (32%), with all mutations in this region involving the S310 codon. Frequent co-altered genes in this cohort were TP53 (54%), PIK3CA (21%), and CDKN2A (18%); KRAS amplification/mutation was found in 7% of patients. One patient with ERBB2 -amplified EHC who enrolled in a basket trial (ClinicalTrials.gov identifier: NCT02675829) had a partial response to the human epidermal growth factor receptor 2–targeted antibody-drug conjugate ado-trastuzumab emtansine. CONCLUSION: ERBB2 alterations are present in 5.4% of BTCs. When present, the degree of ERBB2 gene amplification is often high, and S310 codon mutations are the most common hotspot. These features, along with the presented case, support further development of human epidermal growth factor receptor 2–targeted therapy in ERBB2 -mutant and/or -amplified BTC. [ABSTRACT FROM AUTHOR]

The interplay between surface chemistry and quantum confinement on the band gap energies of indium arsenide (InAs) nanowires is investigated by first principle computations as the surface-to-volume ratio increases with decreasing cross section. Electronic band structures are presented as determined by both density functional and hybrid density functional theory (DFT) calculations; the latter are used to provide improved band gap energy estimates over those from standard approximate DFT methods. Different monovalent chemical species with varying electron affinity are used to eliminate surface states to enable direct comparison between surface chemistry and quantum confinement. The influence of these effects on energy band gaps and electron effective masses is highlighted. It is found that many desirable properties in terms of electronic properties and the elimination of surface states for nanoscale field effect transistors fabricated using [100]-oriented InAs can be achieved. [ABSTRACT FROM AUTHOR]

Cyclin-dependent kinase 4 and 6 inhibitors (CDK4/6i) are key therapeutic agents in the management of metastatic hormone-receptor-positive breast cancer. However, the emergence of drug resistance limits their long-term efficacy. Here, we show that breast cancer cells develop CDK4/6i resistance via a sequential two-step process of E2F activation. This process entails retinoblastoma (Rb)-protein degradation, followed by c-Myc-mediated amplification of E2F transcriptional activity. CDK4/6i treatment halts cell proliferation in an Rb-dependent manner but dramatically reduces Rb-protein levels. However, this reduction in Rb levels insufficiently induces E2F activity. To develop CDK4/6i resistance, upregulation or activating mutations in mitogenic or hormone signaling are required to stabilize c-Myc levels, thereby augmenting E2F activity. Our analysis of pre-treatment tumor samples reveals a strong correlation between c-Myc levels, rather than Rb levels, and poor therapeutic outcomes after CDK4/6i treatment. Moreover, we propose that proteasome inhibitors can potentially reverse CDK4/6i resistance by restoring Rb levels. [Display omitted] • Breast cancer cells develop CDK4/6i resistance via sequential E2F activation • Rb-protein degradation and c-Myc-mediated amplification of E2F activity are key mechanisms • c-Myc levels, not Rb levels, predict poor outcomes after CDK4/6i treatment • Proteasome inhibitors restoring Rb levels can potentially overcome CDK4/6i resistance Kim et al. demonstrate that breast cancer cells develop resistance to CDK4/6 inhibitors through a two-step E2F activation process involving Rb-protein degradation and c-Myc-mediated amplification of E2F activity. They suggest that proteasome inhibitors, which restore Rb levels, could potentially overcome this resistance. [ABSTRACT FROM AUTHOR]

Mutations in ERBB2, the gene encoding epidermal growth factor receptor (EGFR) family member HER2, are common in and drive the growth of "HER2-negative" (not ERBB2 amplified) tumors but are rare in "HER2-positive" (ERBB2 amplified) breast cancer. We analyzed DNA-sequencing data from HER2-positive patients and used cell lines and a patient-derived xenograft model to test the consequence of HER2 mutations on the efficacy of anti-HER2 agents such as trastuzumab, lapatinib, and neratinib, an irreversible pan-EGFR inhibitor. HER2 mutations were present in ~7% of HER2-positive tumors, all of which were metastatic but not all were previously treated. Compared to HER2 amplification alone, in both patients and cultured cell lines, the co-occurrence of HER2 mutation and amplification was associated with poor response to trastuzumab and lapatinib, the standard-of-care anti-HER2 agents. In mice, xenografts established from a patient whose HER2-positive tumor acquired a D769Y mutation in HER2 after progression on trastuzumab-based therapy were resistant to trastuzumab or lapatinib but were sensitive to neratinib. Clinical data revealed that six heavily pretreated patients with tumors bearing coincident HER2 amplification and mutation subsequently exhibited a statistically significant response to neratinib monotherapy. Thus, these findings indicate that coincident HER2 mutation reduces the efficacy of therapies commonly used to treat HER2-positive breast cancer, particularly in metastatic and previously HER2 inhibitor-treated patients, as well as potentially in patients scheduled for first-line treatment. Therefore, we propose that clinical studies testing the efficacy of neratinib are warranted selectively in breast cancer patients whose tumors carry both amplification and mutation of ERBB2/HER2. [ABSTRACT FROM AUTHOR]

Purpose We previously reported the phase I dose escalation study of buparlisib, a pan-class 1A PI3K inhibitor, combined with platinum/taxane-based chemotherapy in patients with advanced solid tumors. The combination was well tolerated and promising preliminary efficacy was observed in PTEN deficient tumors. This phase I dose expansion study now evaluates buparlisib plus high dose carboplatin and paclitaxel in unselected patients with advanced solid tumors and buparlisib plus standard dose carboplatin and paclitaxel in patients with PTEN deficient tumors (ClinicalTrials.gov, NCT01297452). Methods There were two expansion cohorts: Cohort A received continuous buparlisib (100 mg/daily) orally plus high dose carboplatin AUC 6 and paclitaxel 200 mg/m2; Cohort B treated patients with PTEN deficient tumors only and they received the recommended phase II dose (RP2D) of continuous buparlisib (100 mg/daily) orally plus standard dose carboplatin AUC 5 and paclitaxel 175 mg/m2. Both cohorts received chemotherapy intravenously on day 1 of the 21-day cycle with pegfilgrastim support. Primary endpoint in Cohort A was to evaluate the safety and tolerability of chemotherapy dose intensification with buparlisib and in Cohort B was to describe preliminary efficacy of the combination among patients with tumors harboring a PTEN mutation or homozygous deletion. Results 14 subjects were enrolled, 7 in Cohort A and 7 in Cohort B. Dose reductions were required in 5 (71%) and 3 (43%) patients, in cohort A and B respectively. Grade 3 adverse events in Cohort A included lymphopenia ( n = 5 [71%]), hyperglycemia ( n = 2, [29%]), diarrhea ( n = 2, [29%]) and rash ( n = 2, [29%]) and in cohort B included lymphopenia ( n = 5 [71%]), hyperglycemia ( n = 4 [57%]) and neutropenia ( n = 2 [29%]. The mean number of cycles on protocol was 6. The overall objective response rate was 14% (2 /14). No objective responses were observed in the PTEN deficient cohort. Four out of 6 patients with stable disease (SD) had SD or better for ≥6 cycles, 2 of which had PTEN deficient tumors. Conclusion The addition of buparlisib to high dose carboplatin and paclitaxel was not tolerable. The combination did not reveal significant clinical activity amongst a small and heterogenous group of PTEN deficient tumors, [ABSTRACT FROM AUTHOR]

In the mid-1980s, there was a rise in incidence rates of childhood brain tumors (CBT) in the United States that appeared to stabilize at a higher rate in the early 1990s. An updated analysis of the pattern of CBT over the past 2 decades, with commentary on whether the elevated incidence rate has continued, is past due. We used Surveillance, Epidemiology and End Results (SEER) data to examine trends in incidence of CBT from 1973 through 2009. We examined age-adjusted incidence rates (AAIRs) and secular trends for all malignant brain tumors combined (SEER classification) by histologic tumor type and anatomic site. The incidence of CBT remained stable from 1987 to 2009 [annual percent change (APC) = 0.10; 95 % confidence intervals (CI) −0.39 to 0.61] with an AAIR for all CBT of 3.32 (95 % CI 3.22-3.42). The stability of rates in these two decades contrast the change that occurred in the mid-1980s (1983-1986), when the incidence of CBT increased by 53 % (APC = 14.06; 95 % CI 4.05-25.0). From 1983 to 1986, statistically significant rate increases were observed for pilocytic astrocytoma, PNET/medulloblastoma, and mixed glioma. Further, the rate of increase in pilocytic astrocytoma was similar to the rate of decrease for astrocytomas NOS from 1981 to 2009, suggesting a change from a more general to more specific classification. After the increase in rates in the mid-1980s, rates of CBT over the past two decades have stabilized. Changes in incidence rates of subtypes of tumors over this time period reflect changes both in classification of CBT and in diagnostic techniques. [ABSTRACT FROM AUTHOR]

Introduction: Previous studies showed that higher testosterone levels are associated with greater risk of breast cancer in premenopausal women, but the literature is scant and inconsistent. Methods: In a prospective nested case-control study of 104 premenopausal women with incident breast cancer and 225 matched controls, all characterized by regular menstrual cycles throughout their lifetime, we measured the concentration of estradiol, total and free testosterone (FT), progesterone, sex hormone-binding globulin (SHBG), follicle-stimulating hormone (FSH), and luteinizing hormone (LH) in blood samples collected on days 20 through 24 of their cycles. Results: In logistic regression models, the multivariate odds ratios (ORs) of invasive breast cancer for women in the highest tertile of circulating FT compared with the lowest was 2.43 (95% confidence interval (95% CI), 1.15 to 5.10; Ptrend = 0.03), whereas for total testosterone, the association had the same direction but was not statistically significant (OR, 1.27; 95% CI, 0.62 to 2.61; Ptrend = 0.51). Endogenous progesterone was not statistically associated with breast cancer (OR, 1.16; 95% CI, 0.60 to 2.27; Ptrend = 0.75), nor were the other considered hormones. Conclusions: Consistent with previous prospective studies in premenopausal women and our own earlier investigation, we observed that higher levels of FT are positively associated with breast cancer risk in women with regular menstrual cycles throughout their lifetimes. No evidence of risk was found associated with the other endogenous sex steroids. [ABSTRACT FROM AUTHOR]

The effective electron mobility in long-channel silicon-on-insulator junctionless multigate metal-oxide-semiconductor transistors is experimentally studied. It is found that the mobility in heavily doped narrow nanowire (NW) devices at low to moderately high carrier densities significantly exceeds that in wide (planar) devices with the same silicon thickness and doping and, in a certain range of carrier densities, it exceeds the mobility in bulk silicon with the same doping concentration. This effect increases when decreasing the NW width. The possible origins of this effect are discussed. These results are extremely encouraging for the development of junctionless NW transistors. [ABSTRACT FROM AUTHOR]

In this paper we study the influence of emission/absorption processes due to optical phonons on the electrical properties of multigate silicon nanowire transistors. We show that low-energy phonons reduce drain current through backscattering of carriers by emission/absorption processes while high-energy phonons redistribute the current energy spectrum along the nanowire channel through phonon emission without significantly reducing the drain current drive. The influence of emission/absorption is investigated in different multigate silicon FET structures with uniform channel, single impurity, random doping atom distribution and oxide tunnel barriers. A three-dimensional quantum mechanical device simulator based on the NEGF formalism in coupled mode-space approach is used to model electron transport in the presence of optical phonon scattering mechanism. Electron-phonon scattering is accounted for by adopting the self-consistent Born approximation and using the deformation potential theory. [ABSTRACT FROM AUTHOR]

Studies of ethnic disparities in malignancies have revealed variation in clinical outcomes. In multiple myeloma ( MM), previous literature has focused only on patients of Caucasian and African- American ( AA) descent. We present a Surveillance Epidemiology and End Results ( SEER)-based outcome analysis of MM patients from a broader range of ethnicities, representing current United States demographics. The SEER 17 Registry data was utilized to analyse adult MM patients diagnosed since 1992 ( n = 37 963), as patients of other ethnicities were not well represented prior to that. Overall survival ( OS) and myeloma-specific survival ( MSS) were compared across different ethnicities stratified by year of diagnosis, registry identification, age, sex and marital-status. Hispanics had the youngest median age at diagnosis (65 years) and Whites had the oldest (71 years) ( P < 0·001). Increased age at diagnosis was an independent predictor of decreased OS and MSS. Asians had the best median OS (2·7 years) and MSS (4·1 years), while Hispanics had the worst median OS (2·4 years). These trends were more pronounced in patients ≥75 years. Cumulative survival benefit over successive years was largest among Whites (1·3 years) and smallest among Asians (0·5 years). These disparities may be secondary to multifactorial causes that need to be explored and should be considered for optimal triaging of healthcare resources. [ABSTRACT FROM AUTHOR]

We investigated whether variants in sex steroid hormone metabolism genes modify the effect of hormone therapy (HT) on endometrial cancer risk in postmenopausal non-Hispanic white women. A nested case-control study was conducted within the California Teachers Study (CTS). We genotyped htSNPs in six genes involved in the hormone metabolism in 286 endometrial cancer cases and 488 controls. Odds ratio (OR) and 95% confidence interval (CI) were estimated for each haplotype using unconditional logistic regression, adjusting for age. The strongest interaction was observed between duration of estrogen therapy (ET) use and haplotype 1A in CYP11A1 ( pinteraction = 0.0027; pinteraction = 0.010 after correcting for multiple testing within each gene). The OR for endometrial cancer per copy of haplotype 1A was 2.00 (95% CI: 1.05-3.96) for long-term ET users and 0.90 (95% CI: 0.69-1.18) for never users. The most significant interaction with estrogen-progestin therapy (EPT) was found for two haplotypes on CYP19A1 and EPT use (haplotype 4A, pinteraction = 0.024 and haplotype 3B, pinteraction = 0.043). However, neither this interaction, nor the ET or EPT interactions for any other genes, was statistically significant after correction for multiple testing. Variations in CYP11A1 may modify the effect of ET use on risk of postmenopausal endometrial cancer; however, larger studies are needed to explore these findings further. [ABSTRACT FROM AUTHOR]

The purpose of this cross-sectional study on 191 HIV/AIDS patient was to prepare the first Persian translation of complete WHOQOL-HIV instrument, evaluate its reliability and validity, and apply it to determine quality of life and its associated factors in Tehran, Iran. Student's t-test was used to compare quality of life between groups. Mean Cronbach's a of facets in all six domains of instrument were more than 0.6 indicating good reliability. Item/total corrected correlations coefficients had a lower limit of more than 0.5 in all facets except for association between energy and fatigue facet and physical domain. Compared to younger participants, patients older than 35 years had significantly lower scores in overall quality of life (P = 0.003), social relationships (P = 0.021), and spirituality/religion/personal beliefs (P = 0.024). Unemployed patients had significantly lower scores in overall quality of life (P = 0.01), level of independence (P = 0.004), and environment (P = 0.001) compared to employed participants. This study demonstrated that the standard, complete WHOQOL-HIV 120 instrument translated into Farsi and evaluated among Iranian participants provides a reliable and valid basis for future research on quality of life for HIV and other patients in Iran. [ABSTRACT FROM AUTHOR]

This paper presents the evaluation of the analog properties of nMOS junctionless (JL) multigate transistors, comparing their performance with those exhibited by inversion-mode (IM) trigate devices of similar dimensions. The study has been performed for devices operating in saturation as single-transistor amplifiers, and we have considered the dependence of the analog properties on fin width Wfin and temperature T. Furthermore, this paper aims at providing a physical insight into the analog parameters of JL transistors. For that, in addition to device characterization, 3-D device simulations were performed. It is shown that, depending on gate voltage, JL devices can present both larger Early voltage VEA and larger intrinsic voltage gain AV than IM devices of similar dimensions. In addition, VEA and AV are always improved in JL devices when the temperature is increased, whereas they present a maximum value around room temperature for IM transistors. [ABSTRACT FROM AUTHOR]

Night shift work is associated with increased risk of several cancers, but the risk of skin cancer among night shift workers is unknown. We documented 10,799 incident skin cancers in 68,336 women in the Nurses' Health Study from June 1988 to June 2006 and examined the relationship between rotating night shifts and skin cancer. We used Cox proportional hazard models, adjusted for confounding variables (phenotypic and established risk factors of skin cancer), and performed stratified analysis to explore the modifying effect of hair color. Working 10 years or more on rotating night shifts was associated with a 14% decreased risk of skin cancer compared with never working night shifts (age-standardized incidence rate: 976 per 100,000 person-years (PY) vs 1070 per 100,000 PY, respectively; adjusted hazard ratios = 0.86, 95% confidence interval = 0.81 to 0.92, P(trend) < .001). This association was strongest for cutaneous melanoma; working 10 years or more of rotating night shifts was associated with 44% decreased risk of melanoma, after adjustment for melanoma risk factors (age-standardized incidence rate: 20 per 100,000 PY vs 35 per 100,000 PY, respectively; adjusted hazard ratios = 0.56, 95% confidence interval = 0.36 to 0.87, P(trend) = .005). Hair color, a surrogate for an individual's susceptibility to skin cancer, was a statistically significant effect modifier for the observed associations; darker-haired women had the lowest risk (P(interaction) = .02). [ABSTRACT FROM AUTHOR]

Night shift work is associated with increased risk of several cancers, but the risk of skin cancer among night shift workers is unknown. We documented 10 799 incident skin cancers in 68 336 women in the Nurses’ Health Study from June 1988 to June 2006 and examined the relationship between rotating night shifts and skin cancer. We used Cox proportional hazard models, adjusted for confounding variables (phenotypic and established risk factors of skin cancer), and performed stratified analysis to explore the modifying effect of hair color. Working 10 years or more on rotating night shifts was associated with a 14% decreased risk of skin cancer compared with never working night shifts (age-standardized incidence rate: 976 per 100 000 person-years (PY) vs 1070 per 100 000 PY, respectively; adjusted hazard ratios = 0.86, 95% confidence interval = 0.81 to 0.92, Ptrend < .001). This association was strongest for cutaneous melanoma; working 10 years or more of rotating night shifts was associated with 44% decreased risk of melanoma, after adjustment for melanoma risk factors (age-standardized incidence rate: 20 per 100 000 PY vs 35 per 100 000 PY, respectively; adjusted hazard ratios = 0.56, 95% confidence interval = 0.36 to 0.87, Ptrend = .005). Hair color, a surrogate for an individual’s susceptibility to skin cancer, was a statistically significant effect modifier for the observed associations; darker-haired women had the lowest risk (Pinteraction = .02). [ABSTRACT FROM PUBLISHER]

This paper presents the effect of different elastic acoustic and inelastic optical electron–phonon interaction mechanisms on quantum transport and electrical characteristics of multigate silicon nanowire FETs. A 3-D quantum–mechanical device simulator based on the nonequilibrium Green's function formalism in the uncoupled mode space that can handle electron–phonon interactions has been developed to extract the physical parameters of the devices. The electron–phonon scattering has been treated by using the self-consistent Born approximation and deformation potential theory. Utilizing this simulator, we show that interaction of the carriers with optical phonons redistributes the energy and momentum of electrons in the transport direction, depending on the energy of the phonon. Optical phonons cause either a reduction of the electron density or an increase of the electron concentration in the channel region, depending on the phonon energy and coupling strength. Finally, we show that the critical length for carriers to get backscattered in the silicon nanowire is directly proportional to the phonon energy. [ABSTRACT FROM AUTHOR]